Before you can dock a ligand, you will need atom types and charges for every atom in the ligand. It is recommended that you use SYBYL MOL2 format for the ligand file since it contains fields for atom types and charges. For a single ligand (or several ligands), you can use sybyl to prepare a MOL2 file for the ligand.
Check if a database of ligands has already been prepared at your site. Again, we recommend that this database be in SYBYL MOL2 format . If the MOL2 database does not exist, then you will need to construct it. Typically, the Available Chemicals Directory (ACD) is used as a ligand database. This database is distributed by Molecular Design Ltd. (San Leandro, CA) for use with the isis database package. The ACD can be output from isis in an SD-format file. Use sdf2mol2 & sybdb to generate a MOL2 file from the SD file. This conversion requires sybyl (from Tripos) to assign atom types and charges.